Identification of Body Color-Related QTLs in Leopard Coral Grouper (Plectropomus leopardus) Based on GWAS and the HSV Color System

family, is characterized by its distinct red coloration and excellent meat quality, making it one of the most premium species in the grouper market. Body color is an important economic trait for leopard coral grouper because it is an important factor in determining market price. In order to improve the traits in leopard coral grouper, the regulatory mechanism of body color and pigmentation is essential to explore. In the research, QTLs associated with body color in leopard coral grouper were detected using genome-wide association study analysis. A mixed population derived from 12 female and 12 male wild individuals with significant color differences was established. Meanwhile, the HSV (Hue, Saturation, Value) color model was employed to quantify leopard coral grouper body color as continuous variables. In the results, a total of 18 SNPs associated with the body color of the leopard coral grouper were discovered. Through functional annotation, we identified four candidate genes associated with body color: ASAP2, NLRC3, ALDH18A1, and E2F4. These genes were involved in chromatophore distribution, contraction and dilation, carotenoid oxidation, pigment cell proliferation and development, and immune-related processes. These findings uncovered new genetic loci and regulatory mechanisms for body color, providing a genetic basis for understanding pigmentation regulation and supporting marker-assisted selective breeding in leopard coral grouper.